Nucleic Acids in Chemistry and Biology

2.3.5.1 Enzymology of DNA Supercoiling. DNA topoisomers are circular molecules, which have iden- tical sequences and differ only ...

esters to produce an enzyme-bridged gap in both strands. The other DNA duplex is passed through the gap (using energy provided b ...

Hoogsteen hydrogen bonds using N-7 of the purine bases of the Watson–Crick base pairs (Figures 2.33 and 2.34).^36 The resulting ...

homo-pyrimidines and one homo-purine (Figure 2.33c). However, despite the backbone distortion that must result from the hetero-m ...

Several studies on third-strand binding to a homo-purinehomo-pyrimidine duplex have established the following features:
A thi ...

G- and C-rich strands are found at the telomeric ends of chromosomes (see Section 6.4.5), and such sequences are of fundamental ...

structures for G-tetrads have only emerged recently. Dinshaw Patel and co-workers determined the structure of the tetraplex adop ...

gentle right-handed helical twist (12°–20°, the rise is 6.2 Å) between covalently linked residues gives the C-rich quadruplex a ...

is now possible to predict double-helical sections by computer analysis of primary sequence data, and this technique has been us ...

2.4.2 Secondary Structure of RNA: A-RNA and A

-RNA Two varieties of A-type helices have been observed for fibres of RNA species ...

12 bp per turn of the duplex. Both structures have typical Watson–Crick base pairs, which are displaced 4.4 Å from the helix axi ...

helix twist and in base pair roll, slide and propeller twist (Figure 2.19). The extent of variation from base to base is much le ...

with chemical modifications in the phosphate, sugar or base moieties (Section 4.4). In some cases, the result- ing hetero-duplex ...

RNase H^59 and the RNase H domain from HIV-1 reverse transcriptase,^60 and hybrid duplexes have revealed that the RNA adopts a s ...

suggests that there is probably a high level of order in such loops, notably of base-stacking and base-triples. One general opin ...

2.4.4.1 Thermodynamics of Secondary Structure Elements. The free energy of an RNA conform- ation has to take into account the co ...

result of both NMR and X-ray analysis. However, the computer prediction of tertiary interactions and base-triples appears to be ...

cases, the shape of the melting curve can be analysed to identify several components of defined compos- ition melting in series. ...

nucleation is rate-limiting at low concentrations and each duplex zips to completion almost instantly ( 1000 bp s^1 ). The nucle ...

at temperatures well below the melting temperature to give local, short-range separation of the strands. This readily reversible ...